Vaisheshika, or Vaiśeṣika, is one of the six Hindu schools of philosophy of ancient India. Historically, it has been closely associated with the Hindu school of logic, Nyaya Vaisesika philosophy of atomism is that all objects in the physical universe are reducible to a finite number of atoms. This school of philosophy traces its origin to the sage Kaṇāda or Kana-bhuk, translated into English as atom-eater, around the 2nd century BC

Vaiseshika's Atomic theory.
Dakshinamurti Stotra of Shri Shankaracharya translated by Alladi Mahadeva Sastry
The paramanus, the extremely small atoms, combined together, constitute the upâdâna or material cause of the universe. Hence it is that a pot manifests itself in constant association with clay, but not with Isvara. It is the indivisible extremely subtle things called paramanus, which, combining together in various ways, give rise to the universe comprising all created objects with their attributes and activities. We speak of a substance as the upadana or material cause of other things when it is found invariably associated with them, and upon whose existence the existence of those other things depends. Nothing in our experience is thus invariably found associated with Atman, the Self, or Isvara. On the other hand, every created object is found invariably associated with something other than Atman, with something or other, which is insentient. A pot, for instance, is invariably associated with clay. Hence the conclusion that the insentient atoms, not the sentient Isvara nor His Maya, are the material cause of the universe. It is the qualities, such as color, taste, etc., inherent in the atoms themselves, which produce qualities of a kindred sort in the effect separately. Thus, the atoms and their qualities give rise to all objects in creation as well as their qualities, so that Isvara is not the material cause either of the substances or of their qualities.

Vaiseshika's threefold cause.

Indian Atom 3D 
That with which the effect is intimately associated is the samavâyi-kârana, the inseparable or material cause, as. opposed to the accessories such as the potter's wheel, which belong to a category different from the samavâyi-kârana. That is said to be the asamavayi-karana, the accidental or separable cause, which, while quite necessary to produce the effect, resides in the samavâyi, or in the substratum of the samavâyi. An efficient (nimitta) cause of all effects is Isvara, like the potter. The Vaiseshika says that there are three kinds of causes for every positive effect, known respectively as the samavayi or upadana-karana, the material cause; the asamavayi-karana, the accidental cause; the nimitta-karana, the efficient or intelligent cause. Thread is the material cause of a cloth, because the latter is in constant relation with the other. According to the definition of the asamavayi-karana given in the verse 4, the combining of threads with one another constitutes the asamavayi-karana of the cloth, because the act of combining resides in the threads, which form the samavayi-karana of the cloth. Again, according to the definition, the color of the thread is the asamavayi-karana of the color of the cloth, because the former which gives rise to the latter resides in the thread which forms the substratum (the samavayin) of the cloth, and the cloth again is the substance wherein the color of the cloth inheres in constant relation and is therefore called the samavayi of that color. The remaining factors in the causal aggregate comprise (1) what is called the nimitta-karana, the efficient cause like the weaver, and (2) the sahakari or auxiliary cause such as the instruments used by him in producing the cloth out of the thread. Isvara is said to be a mere efficient cause in all effects. And as the efficient cause He is a necessary factor in the creation of the universe; for, we see that without an impulse from a sentient being no effect is ever produced out of a material. Without a potter, for instance, no pot is ever produced out of clay. Isvara being thus only one of the factors in the creation of the universe, to hold that the sole cause of the universe is the sentient Brahman is opposed to all our experience. Whencesoever an effect is born, there it abides; a pot abides in clay, a cloth in thread, a finger-ring in gold. Thus say the Vaiseshikas as well as the Naiyâyikas.

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